Dear Glenn

The positive attribute hasn't been extended to data variables in CF because
the standard name always implies the sign convention e.g.
  toa_net_downward_longwave_flux
  toa_net_upward_shortwave_flux
The advantage of doing it is this way is that it is impossible for the sign
convention to be missing if the quantity is identified by standard name! I am
not clear about the details of your case, but I guess that it should be
possible to use a standard name which states what the sign convention is for
the thickness of the water column.

Best wishes

Jonathan
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